FROGS Phyloseq: Visualize Data Composition (version 3.2)

Phyloseq 1.30.0

## Import functions
library(plotly)
library(phyloseq)
source(file.path(params$libdir, "graphical_methods.R")) 
## Alternative to source all extra function from a github repo
# source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R")

## Setting variables
  ## Phyloseq object (rdata file)
  # phyloseq <- ""
  
  ## Experimental variable used to group samples (Treatment, Host type, etc).
  # varExp <- "" 
  
  ## Taxonomic level to filter your data" help="ex: Kingdom, Phylum, Class, Order, Family, Genus, Species
  # taxaRank1 <- ""
  
  ## Taxa (at the above taxonomic level) to keep in the dataset"
  ## ex: Bacteria (when filtering at the Kingdom level), Firmicutes (when filtering at the Phylum level). 
  ## Multiple taxa (separated by a space) can be specified, i.e. Firmicutes Proteobacteria 
  # taxaSet1 <- "" 
  
  ## Taxonomic level used for aggregation" help="ex: Family (when filtering at the Phylum level). 
  ## The aggregation level must be below the filtering level.
  # taxaRank2 <- ""
  
  ## Number of most abundant taxa to keep", 
  ## ex: 9, i.e. Tool keeps the 9 most abundant taxa and the remaining taxa are aggregated in a group 'Other
  # numberOfTaxa = 

  ## Create input and parameters dataframe
  # params <- data.frame("phyloseq"=phyloseq, 
  #                      "varExp"=varExp, 
  #                      "taxaRank1" = taxaRank1, 
  #                      "taxaSet1" = taxaSet1, 
  #                      "taxaRank2" = taxaRank2, 
  #                      "numberOfTaxa"=numberOfTaxa )

## Load Phyloseq object
load(params$phyloseq)

# custum graphical facetting
facet <- paste('facet_wrap(~', params$varExp,', scales = "free_x", nrow = 1)')

Bar plot

p <- plot_bar(data,fill= rank_names(data)[2]) + eval(parse(text = facet)) + 
        ggtitle(paste("Bar plot colored by", rank_names(data)[2])) + 
        theme(plot.title = element_text(hjust = 0.5))
plot(p)

Composition plot

taxaSet1 <- unlist(strsplit(params$taxaSet1, " "))
p        <- plot_composition(data, params$taxaRank1, taxaSet1, params$taxaRank2, params$numberOfTaxa, fill=params$taxaRank2) 
p        <- p + eval(parse(text = facet)) + theme(plot.title = element_text(hjust = 0.5))

gp <- ggplotly(p, tooltip = c("x", "y", "fill"))
gp$x$layout$annotations[[1]]$x <- -0.08
gp$x$layout$margin$l = 75
gp$x$layout$margin$b = 100
gp$x$layout$margin$t = 100
gp